CODEWITHSUNDEEP
rdplyrtidy
user468311
user468311

Reputation:

Can't rename columns with dplyr

I'm trying to rename columns in data frame from Characteristics..genotype. to genotype and from Characteristics..age. to age:

pData(raw_data) %>%
  rename(
    age = Characteristics..age.,
    genotype = Characteristics..genotype.
  )

I get the following error:

Error in rename(., age = Characteristics..age., genotype = Characteristics..genotype.) : object 'Characteristics..age.' not found

Which doesn't make sense since columns exist in the data frame:

pData(raw_data)$Characteristics..genotype.

Output of the above:

[1] N171-HD82Q N171-HD82Q N171-HD82Q wt wt wt N171-HD82Q N171-HD82Q N171-HD82Q wt wt
[12] wt N171-HD82Q N171-HD82Q N171-HD82Q wt wt wt
Levels: N171-HD82Q wt

What am I missing?

Upvotes: 0

Views: 4616

Answers (2)

IceCreamToucan
IceCreamToucan

Reputation: 28705

You could use rename_all and do the renaming with a function, e.g. use stringr::str_remove_all to remove all instances of "Characteristics.." at the start or "." at the end (periods escaped with \\).

library(tidyverse) # dplyr and stringr
df %>% 
  rename_all(str_remove_all, '^Characteristics\\.\\.|\\.$')

Upvotes: 3

akrun
akrun

Reputation: 887951

An option would be backquotes

library(dplyr)
 pData(raw_data) %>%
  rename(
    age = `Characteristics..age.`,
   genotype = `Characteristics..genotype.`
  )

Or based on the error (reproduced with plyr::rename), it would be better to use :: to specify the package from which it loads to avoid masking

pData(raw_data) %>%
  dplyr::rename(
    age = Characteristics..age.,
   genotype = Characteristics..genotype.
  )

But, while testing on dplyr_0.8.3, it is working fine without backquotes a well

data(mtcars)
raw_data <- head(mtcars)
names(raw_data)[1] <- "Characteristics..genotype."
raw_data %>%
      dplyr::rename(genotype = Characteristics..genotype.)
#             genotype cyl disp  hp drat    wt  qsec vs am gear carb
# ...

The issue would be that plyr also include the same rename function, so if the package was also loaded, it could mask the dplyr::rename

raw_data %>% 
    plyr::rename(genotype = Characteristics..genotype.)

Error in plyr::rename(., genotype = Characteristics..genotype.) :
unused argument (genotype = Characteristics..genotype.)

Upvotes: 5

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